Abstract: I propose to study through which molecular mechanisms of genetic control it is that large genomic Copy Number Variants (CNVs) exert their effects on gene regulation, dynamically over cellular differentiation and cellular functioning. We aim to establish a novel research program and paradigm in our laboratory that combines the use of induced Pluripotent Stem Cells (iPSC) and multi-level, comprehensive and integrated analysis of genomic and epigenomic layers of control and activity. In the process we will be testing several novel hypotheses on the molecular mechanisms through which CNVs affect gene regulation and thus cellular and eventually organismal phenotypes. This will also serve as a model for smaller CNVs and their potentially subtle and cumulative or combinatorial yet potentially substantive effects on phenotype in health and disease. Copy Number Variation (CNV) is common in the genome of healthy humans and is associated with phenotypic variation. CNV is also frequently and strongly associated with major disease phenotypes, especially in neuropsychiatric diseases that involve an aberrant development of the brain such as schizophrenia and autism. There are now several prominent examples for CNVs that are strongly associated with neuropsychiatric disorders such as schizophrenia, autism, mental retardation and epilepsy (22q11.2 deletions, 1q21.1 deletions and duplications, 15q13.3 deletions, 16p11.2 deletions and duplications, 3q29 microduplications). CNVs (and sometimes the same CNVs as mentioned above) are also strongly associated with malformation diseases of the heart as well as in phenotypes that involve the functioning of the immune system. CNVs are therefore an important phenomenon to study both in its own right as a strong predisposing factor for disease as well as an enticing point of entry for the better understanding of the molecular etiology of complex diseases with a strong and complex genetic and genomic component. A major barrier to a better understanding of how the molecular mechanisms through which CNV affect phenotype is the lack of access to relevant human tissues that carry a given disease associated CNV, for example neuronal tissue cultures with a large genomic deletion that is strongly associated with schizophrenia or autism. The use of iPSC lines from probands with a given CNV promises to overcome this barrier and will allow us to observe the effects of CNVs on a molecular level in the relevant tissue as it progresses along a developmental trajectory and then settles into the neuronal phenotype. The complete and multilevel high-resolution genomics and epigenomics analyses based on massively parallel DNA next-generation-sequencing will include comprehensive transcriptome analyses by RNA-Seq, meDNA- Seq to study DNA methylation patterns and ChIP-Seq to map regulatory histone modifications and transcription factor networks. Public Health Relevance: Neurodevelopmental, neuropsychiatric disorders such as schizophrenia and autism spectrum disorders are a major public health concern. Copy Number Variations are amongst the candidate loci with the strongest association with such diseases but they typically affect multiple genes and only very little basic knowledge about their molecular mechanisms of action exists. Our project will create a new research paradigm into the effects of CNV during neuronal development by combining iPSC techniques with comprehensive nextgeneration genomics analyses.